Synonymous codon usage pattern in glycoprotein gene of rabies virus

Morla, Sudhir; Makhija, Aditi; Kumar, Sachin

doi:10.1016/j.gene.2016.02.047

Cited by 92 publications

(54 citation statements)

References 32 publications

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“…The ENC is considered the magnitude of the codon usage bias of a single gene (Wright, 1990). The ENC value is not influenced by the amino acid or the gene length (Morla et al, 2016) . The ENC value was calculated using the formula given below:…”

Section: Effective Number Of Codons (Enc)mentioning

confidence: 99%

Analysis of the codon usage of the ORF2 gene of feline calicivirus

Zang

et al. 2017

Infection, Genetics and Evolution

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Feline calicivirus (FCV) is a highly prevalent pathogen of the domestic cat that causes acute infections of the oral and upper respiratory tract. The E region of the ORF2 protein is responsible for the induction of virus-neutralizing antibodies, thus it is important to understand the codon usage of this gene. Here, analysed 90 coding sequences of ORF2 and show that it undergoes a low codon usage bias. In addition, although mutational bias is one of the factors shaping the codon usage bias of this gene, natural selection plays a more significant role. Our results reveal part of the mechanisms driving FCV evolution, which will lay foundation for the further research of FCV.

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Section: Effective Number Of Codons (Enc)mentioning

confidence: 99%

Analysis of the codon usage of the ORF2 gene of feline calicivirus

Zang

et al. 2017

Infection, Genetics and Evolution

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“…Satisfactorily, the obtained CAI value (0.986) was very close to 1.0 and GC contents (56.60%) was also within the optimal limit (30-70%) indicating possible higher expression within E. coli K12 system (Shey et al 2019;Morla, Makhija, and Kumar 2016). As a suggestion for prospective vaccine synthesis, in silico cloning was also performed using pET30a(+) vector.…”

Section: Discussionmentioning

confidence: 66%

“…The codon adaptation index (CAI) value (Sharp and Li 1987) and guanine-cytosine (GC) content of the adapted sequence were calculated. The CAI score is the measure of codon usage biasness and an optimal CAI score should be 1.0 but score greater than 0.8 can be considered as good (Morla, Makhija, and Kumar 2016). An optimal score of GC content range in between 30-70%…”

Section: Codon Adaptation and In Silico Cloningmentioning

confidence: 99%

Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans – An Integrated Vaccinomics Approach

Nain

Karim

Sen³

et al. 2019

Preprint

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Buruli ulcer is an emerging-necrotizing skin infection, responsible for permanent deformity if untreated, caused by the pathogen Mycobacterium ulcerans (M. ulcerans). Despite this debilitating condition, no specific disease-modifying therapeutics or vaccination is available. Therefore, we aimed to design an effective multi-epitope vaccine against M.ulcerans through an integrated vaccinomics approach. Briefly, the highest antigenic PE-PGRS protein was selected from which the promiscuous T-and B-cell epitopes were predicted. After rigorous assessment, 15 promising CTL, HTL and LBL epitopes were selected. The identified T-cell epitopes showed marked interactions towards the HLA binding alleles and provided 99.8% world population coverage. Consequently, a vaccine chimera was designed by connecting these epitopes with suitable linkers and adjuvant (LprG). The vaccine construct was antigenic and immunogenic as well as non-allergenic; hence, subjected to homology modelling. The molecular docking and dynamic simulation revealed strong and stable binding affinity between the vaccine and TLR2 receptor. The binding energy (∆G) and dissociation constant (Kd) were -15.3 kcal/mol and 5.9×10 -12 M, respectively. Further, disulfide engineering was applied to improve vaccine' stability and higher expression in Escherichia coli K12 system was ensured by codon optimization and cloning in silico.The computer-simulated immune responses were characterized by higher levels of IgM and IgG antibodies,helper T-cells with increased IFN-γ production, and macrophage activity crucial for immunity against M. ulcerans.Therefore, our data suggest that, if the designed vaccine is validated experimentally, it will prevent Buruli ulcer by generating robust immune response against M. ulcerans.

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“…We calculated ENC values and nucleotide composition and found that the highest mean ENC value was for RABV (53.84), indicating that the codon usage bias of RABV was the lowest. Previous studies have already reported low codon usage bias for RABV genes including, N [32] and G [33]. In addition, low codon usage bias has been identified in other RNA viruses, such as H5N1 influenza virus (50.91) [34], H3N8 Equine influenza virus (52.09) [35], Ebola virus (57.23) [36] and hepatitis C virus (HCV) (52.62) [37].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

Zhang

Cai

Zhai

et al. 2018

IJMS

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Rabies virus (RABV) and other lyssaviruses can cause rabies and rabies-like diseases, which are a persistent public health threat to humans and other mammals. Lyssaviruses exhibit distinct characteristics in terms of geographical distribution and host specificity, indicative of a long-standing diversification to adapt to the environment. However, the evolutionary diversity of lyssaviruses, in terms of codon usage, is still unclear. We found that RABV has the lowest codon usage bias among lyssaviruses strains, evidenced by its high mean effective number of codons (ENC) (53.84 ± 0.35). Moreover, natural selection is the driving force in shaping the codon usage pattern of these strains. In summary, our study sheds light on the codon usage patterns of lyssaviruses, which can aid in the development of control strategies and experimental research.

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Synonymous codon usage pattern in glycoprotein gene of rabies virus

Cited by 92 publications

References 32 publications

Analysis of the codon usage of the ORF2 gene of feline calicivirus

Analysis of the codon usage of the ORF2 gene of feline calicivirus

Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans – An Integrated Vaccinomics Approach

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

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